The breast-specific proteome
The human breast consists mainly of skin, adipose and glandular tissue with the main purpose to provide milk for a newborn child. Transcriptome analysis shows that 72% (n=14418) of all human proteins (n=20090) are expressed in the breast and 135 of these genes show an elevated expression in the breast compared to other tissue types.
The breast transcriptome
Transcriptome analysis of the breast can be visualized with regard to the specificity and distribution of transcribed mRNA molecules (Figure 1). Specificity illustrates the number of genes with elevated or non-elevated expression in the breast compared to other tissues. Elevated expression includes three subcategory types of elevated expression:
Distribution, on the other hand, visualizes how many genes have, or do not have, detectable levels (nTPM≥1) of transcribed mRNA molecules in the breast compared to other tissues. As evident in Table 1, all genes elevated in breast are categorized as:
Figure 1. (A) The distribution of all genes across the five categories based on transcript specificity in breast as well as in all other tissues. (B) The distribution of all genes across the six categories, based on transcript detection (nTPM≥1) in breast as well as in all other tissues.
As shown in Figure 1, 135 genes show some level of elevated expression in the breast compared to other tissues. The three categories of genes with elevated expression in breast compared to other organs are shown in Table 1. In Table 2, the 12 genes with the highest enrichment in breast are defined.
Table 1. The number of genes in the subdivided categories of elevated expression in breast.
Protein expression of genes elevated in breast
In-depth analysis of the elevated genes in smooth muscle using antibody-based protein profiling allowed us to visualize the expression patterns of these proteins in different functional compartments.
Mammary glands in the fully developed breast can either be lactating or non-lactating. During pregnancy, non-lactating mammary glands undergo morphological alterations through the influence of hormonal changes in the body to become active and start the lactation process in order to provide milk for infants. Some proteins can therefore only be detected after this transformation. An example of a protein expressed in lactating breast is alpha-lactalbumin (LALBA), a principal protein of milk required for lactose synthesis in the mammary gland.
Figure 2. Immunohistochemical staining of human lactating breast using an antibody toward LALBA.
Table 3. Following 10 genes have been analyzed in breast.
Gene expression shared between the breast and other tissues
There are 36 group enriched genes expressed in breast. Group enriched genes are defined as genes showing a 4-fold higher average level of mRNA expression in a group of 2-5 tissues, including breast, compared to all other tissues.
To illustrate the relation of breast tissue to other tissue types, a network plot was generated, displaying the number of genes with a shared expression between different tissue types.
Figure 3. An interactive network plot of the breast enriched and group enriched genes connected to their respective enriched tissues (grey circles). Red nodes represent the number of breast enriched genes and orange nodes represent the number of genes that are group enriched. The sizes of the red and orange nodes are related to the number of genes displayed within the node. Each node is clickable and results in a list of all enriched genes connected to the highlighted edges. The network is limited to group enriched genes in combinations of up to 3 tissues, but the resulting lists show the complete set of group enriched genes in the particular tissue.
One example of a group enriched gene in breast and other tissues is Keratin 15 (KRT15). Keratins are intermediate filament proteins responsible for the structural integrity of epithelial cells. Keratin 15 (KRT15) show elevated expression in breast, esophagus, skin and vagina.
Hormone receptors in breast
The function of the breast is dependent on steroid hormones like progesterone, prolactin, placental lactogen and estrogen, which acts through their respective receptors in the mammary epithelium. One example is Estrogen receptor 1, ESR1, a receptor present in female tissues, where it links estrogen hormones and transmit the signal to alter the activity of genes in the nucleus. ESR1 shows distinct nuclear positivity in breast, fallopian tube, cervix and endometrium.
Proteins analyzed in extended samples of lactating breast
The standard setup in the Tissue Atlas is based on the Tissue Microarray (TMA) technique, thus saving valuable tissue material as well as reagents and provides a wide tissue representation for protein profiling. In addition to the standard setup, extended tissue profiling in breast is performed for selected proteins, to give a more complete overview on where the proteins is expressed. The full list of genes used for protein profiling on breast samples is defined in Table 3.
Table 4. Following 10 genes have been analyzed in lactating breast.
The primary function of the breast is to provide milk for the newborn infant. The mammary gland is a complex structure that includes a layer of secretory epithelial cells that secrete milk into the ducts and cavities by mechanisms such as exocytosis of secretory vesicles and budding-off of milk fat globules. The milk producing acinar cells are covered in a surrounding layer of myoepithelial cells that eject milk through contraction.
The main components of the human breast consists of the skin, subcutaneous adipose tissue and glandular tissue. Before puberty, the breasts are a very basic construct; a nipple connected to a simple duct system. During puberty, the breasts transform under the influence of hormones that lead to an increase in adipose tissue and complex branching of the previous basic ductal system. Below the nipple, the collecting ducts dilate to form the lactiferous sinuses. The breast is divided into 15-25 lobes, each based on a branching duct system that leads from the collecting ducts to the terminal duct lobular units. The terminal duct-lobular units are the functional sites of milk production. Each collecting duct drains a lobe made up of 20-40 lobules. In addition to glandular cells, the lobe is composed chiefly of adipose tissue and fibrous stroma - referred to as the inter- and perilobular connective tissue.
In the nipple, the stratified squamous epithelium from the surface extends into the collecting ducts for a variable short distance. There is then an abrupt change into the glandular epithelium that is present throughout the duct and lobular system. The glandular epithelium is composed of two distinct types of cells, the secretory or luminal cells and myoepithelial cells. In the collecting ducts, the lining cells are usually columnar whereas in the acini they are usually cuboidal. The two types of luminal secretory cells that have been identified are basal cells, which have relatively clear cytoplasm and an oval nucleus lacking a visible nucleolus, and the superficial luminal cells with darker, basophilic cytoplasm. The myoepithelial cells usually form a discontinuous layer between the luminal secretory cells and the basement membrane. The myoepithelial cells appear small, flattened and with dark nuclei.
Here, the protein-coding genes expressed in breast are described and characterized, together with examples of immunohistochemically stained tissue sections that visualize corresponding protein expression patterns of genes with elevated expression in breast.
Transcript profiling was based on a combination of two transcriptomics datasets (HPA and GTEx), corresponding to a total of 14590 samples from 54 different human normal tissue types. The final consensus normalized expression (nTPM) value for each tissue type was used for the classification of all genes according to the tissue-specific expression into two different categories, based on specificity or distribution.
Relevant links and publications
Uhlén M et al., Tissue-based map of the human proteome. Science (2015)